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@phac-nml

National Microbiology Laboratory

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  1. staramr staramr Public

    Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

    Python 187 29

  2. mob-suite mob-suite Public

    MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

    Python 170 33

  3. ecoli_serotyping ecoli_serotyping Public

    In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping

    Python 65 11

  4. irida irida Public

    Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology

    Java 43 32

  5. refseq_masher refseq_masher Public

    Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database

    Jupyter Notebook 43 4

  6. sistr_cmd sistr_cmd Public

    SISTR (Salmonella In Silico Typing Resource) command-line tool

    Python 32 9

Repositories

Showing 10 of 160 repositories
  • irida-next Public

    IRIDA Next

    phac-nml/irida-next’s past year of commit activity
    Ruby 13 Apache-2.0 3 6 21 Updated Feb 27, 2026
  • arboratornf Public

    EPS suite Arborator pipeline

    phac-nml/arboratornf’s past year of commit activity
    Nextflow 0 MIT 0 8 0 Updated Feb 27, 2026
  • staramr Public

    Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

    phac-nml/staramr’s past year of commit activity
    Python 187 Apache-2.0 29 19 1 Updated Feb 27, 2026
  • fetchdatairidanext Public

    Pipeline for downloading data from INSDC databases for IRIDA Next.

    phac-nml/fetchdatairidanext’s past year of commit activity
    Nextflow 0 MIT 2 3 1 Updated Feb 27, 2026
  • mikrokondo Public

    A simple pipeline for bacterial assembly and quality control

    phac-nml/mikrokondo’s past year of commit activity
    Nextflow 16 MIT 4 18 1 Updated Feb 26, 2026
  • phac-nml/metadatatransformation’s past year of commit activity
    Nextflow 0 MIT 0 3 0 Updated Feb 26, 2026
  • arborator Public
    phac-nml/arborator’s past year of commit activity
    Python 3 Apache-2.0 1 8 2 Updated Feb 26, 2026
  • viralassembly Public

    Assemble and QC viral reads with a reference scheme

    phac-nml/viralassembly’s past year of commit activity
    Nextflow 1 MIT 1 0 2 Updated Feb 26, 2026
  • submitdatairidanext Public

    Pipeline for submitting data to INSDC databases for IRIDA Next

    phac-nml/submitdatairidanext’s past year of commit activity
    Nextflow 1 MIT 0 3 1 Updated Feb 25, 2026
  • venae Public

    A workflow to rapidly identify species and antimicrobial resistance genes in positive blood cultures sequenced using Oxford Nanopore Technologies (ONT)

    phac-nml/venae’s past year of commit activity
    HTML 1 Apache-2.0 0 0 0 Updated Feb 25, 2026